I believe P&D Hobby sells pilots for F and E units that can be glued right to the bodies. They have smaller openings if you want to put a dummy or kadee coupler or you can get a cover to close the opening. This K-Line E unit has a P&D pilot with coupler cover. Just google P&D hobby and go to their two rail detail part section.
Note I think all of their pilots are the passenger style. To keep the freight style you will probably have to remount the existing one with a spacer to fill the gap.
Pete